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10 sources retrieved · Most recent: April 2026 · Index updated 14 days ago
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RCL1
RNA terminal phosphate cyclase like 1
Chromosome 9 · 9p24.1
NCBI Gene: 10171Ensembl: ENSG00000120158.12HGNC: HGNC:17687UniProt: Q5VZU3
95PubMed Papers
20Diseases
0Drugs
1Pathogenic Variants
FUNCTIONAL ROLE
Hub Gene
DATA QUALITY
✓ Experimental GO Evidence✓ Swiss-Prot Reviewed
ribosomal small subunit biogenesisprotein bindingsmall-subunit processomeendonucleolytic cleavage in 5'-ETS of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)Thrombocytopeniapsychosishemorrhagic diseasethrombocytopenia 4
✦AI Summary

RCL1 (RNA terminal phosphate cyclase like 1) is a nucleolar protein essential for ribosomal small subunit (40S) biogenesis. As a core component of the SSU processome, RCL1 functions in early pre-rRNA processing at sites A0, A1, and A2, promoting proper maturation of 18S rRNA 1. RCL1 activates the GTPase BMS1 by facilitating GDP/GTP exchange, though notably lacks cyclase activity despite its nomenclature. Critically, RCL1's stability and nucleolar localization depend entirely on its interaction with BMS1; without this binding, RCL1 undergoes ubiquitin-proteasome degradation 1. Beyond ribosome biogenesis, RCL1 has emerged as clinically significant in neuropsychiatric disease. A rare missense variant (rs115482041) segregates with depression across multiple family generations, explaining 2.9% of genetic variance and showing significant association in independent populations 2. RCL1 demonstrates striking co-localization with specialized astrocytes in primate brains, suggesting neurodevelopmental relevance 2. Additionally, RCL1 copy number variations associate with diverse neuropsychiatric phenotypes including catatonia, hallucinations, and cognitive decline 3. Non-coding variants in RCL1 influence neutrophil GM-CSF signaling in inflammatory bowel disease 4, and RCL1 is prioritized among 24 genes implicated in chromosome 9 deletion syndrome affecting multiple organ systems 5.

Sources cited
1
RCL1 is a core SSU processome component essential for 18S rRNA processing and maturation; its stability and nucleolar entry depend on BMS1 interaction
PMID: 37451810
2
A rare missense RCL1 variant (rs115482041) segregates with depression and shows significant association in multiple populations; RCL1 colocalizes with primate-specific astrocytes
PMID: 28322274
3
RCL1 copy number variations are associated with diverse neuropsychiatric phenotypes including catatonia, hallucinations, and cognitive decline
PMID: 33597717
4
RCL1 is one of 24 important genes identified in chromosome 9p deletion syndrome affecting the majority of affected individuals
PMID: 40196253
5
Non-coding RCL1 variants are significantly associated with neutrophil GM-CSF signaling variation in inflammatory bowel disease
PMID: 31235766
Disease Associationsⓘ20
ThrombocytopeniaOpen Targets
0.43Moderate
psychosisOpen Targets
0.33Weak
hemorrhagic diseaseOpen Targets
0.26Weak
thrombocytopenia 4Open Targets
0.26Weak
renal osteodystrophyOpen Targets
0.19Weak
liver diseaseOpen Targets
0.10Weak
hepatocellular carcinomaOpen Targets
0.10Suggestive
neoplasmOpen Targets
0.05Suggestive
Abnormal male internal genitalia morphologyOpen Targets
0.05Suggestive
Dupuytren ContractureOpen Targets
0.04Suggestive
hypertensionOpen Targets
0.03Suggestive
depressive disorderOpen Targets
0.03Suggestive
cancerOpen Targets
0.03Suggestive
hypothyroidismOpen Targets
0.02Suggestive
benign neoplasmOpen Targets
0.02Suggestive
intestinal diseaseOpen Targets
0.02Suggestive
brain aneurysmOpen Targets
0.02Suggestive
type 2 diabetes mellitusOpen Targets
0.02Suggestive
preeclampsiaOpen Targets
0.02Suggestive
tibia fractureOpen Targets
0.02Suggestive
Pathogenic Variants1
NM_005772.5(RCL1):c.370C>T (p.Gln124Ter)Pathogenic
Psychotic disorder
☆☆☆☆2020→ Residue 124
View on ClinVar ↗
Related Genes
BRD10Co-mentioned in literature100%ZNG1ACo-mentioned in literature100%NLE1Protein interaction100%WDR18Protein interaction100%DHX37Protein interaction100%GRWD1Protein interaction100%
Tissue Expression6 tissues
Liver
100%
Bone Marrow
68%
Ovary
26%
Lung
22%
Heart
13%
Brain
13%
Gene Interaction Network
Click a node to explore
RCL1BRD10ZNG1ANLE1WDR18DHX37GRWD1
PROTEIN STRUCTURE
Preparing viewer…
PDB7MQA · 2.70 Å · EM
View on RCSB ↗
Constraintⓘ
LOEUFⓘ
0.83LoF Tolerant
pLIⓘ
0.01Tolerant
Observed/Expected LoF0.52 [0.34–0.83]
RankingsWhere RCL1 stands among ~20K protein-coding genes
  • #5,057of 20,598
    Most Researched95 · top quartile
  • #4,907of 5,498
    Most Pathogenic Variants1
  • #7,053of 17,882
    Most Constrained (LOEUF)0.83
Genes detectedRCL1
Sources retrieved10 papers
Response time—
📄 Sources
10▼
1
Stability and function of RCL1 are dependent on the interaction with BMS1.
PMID: 37451810
J Mol Cell Biol · 2024
1.00
2
Whole-Genome Sequencing Reveals Individual and Cohort Level Insights into Chromosome 9p Syndromes.
PMID: 40196253
medRxiv · 2025
0.90
3
Interaction between Bms1 and Rcl1, two ribosome biogenesis factors, is evolutionally conserved in zebrafish and human.
PMID: 27474224
J Genet Genomics · 2016
0.80
4
A rare missense variant in RCL1 segregates with depression in extended families.
PMID: 28322274
Mol Psychiatry · 2018
0.70
5
Whole-genome sequencing reveals individual and cohort level insights into chromosome 9p syndromes.
PMID: 41137173
Genome Med · 2025
0.60